Systems and methods for analyzing microarrays

ABSTRACT

The present invention discloses methods and systems for analyzing microarray data. The method includes the general steps of providing microarray data, normalizing the data using a least trimmed squares regression, and then analyzing the normalized microarray data to obtain a desired result such as an expression profile. There is also disclosed a method of subdividing an array into subarrays before normalization. This approach provides a method for improving measurement accuracy and salvaging array data from arrays containing minor defects. Also disclosed is a Probe-Treatment-Reference (PTR) model for streamlining normalization and summarization of microarray data by allowing multiple references. Other aspects of the present invention include computer systems and computer readable media encoding methods of the present invention.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims an invention which was disclosed in ProvisionalApplication No. 60/828,029 filed Oct. 3, 2006, entitled “ACCURATE ANDJUSTIFIABLE MODULE FOR ANALYZING AFFYMETRIX GENECHIP MEASUREMENT”. Thebenefit under 35 USC §119(e) of the United States provisionalapplication is hereby claimed.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH AND DEVELOPMENT

The present invention is made, at least in part, with the support of NIHgrant R01 GM75308-01. The government has certain rights in theinvention.

FIELD OF THE INVENTION

The invention pertains to the field of microarray data analysis. Moreparticularly, the invention relates to methods for analyzing microarraydata and computer software and systems for performing the methods.

BACKGROUND OF THE INVENTION

DNA Microarrays are miniature arrays containing gene fragments that areeither synthesized directly onto or spotted onto glass or othersubstrates. Thousands of genes may be represented in a single array. Atypical gene expression microarray experiment involves the followingsteps: (1) Preparation of fluorescently labeled target from RNA isolatedfrom the biological specimens; (2) Hybridization of the labeled targetto the microarray; (3) Washing, staining, and scanning of the array; (4)Analysis of the scanned image; and (5) Generation of gene expressionprofiles (see FIG. 1).

Currently two main types of DNA microarrays are being widely used inbiomedical applications: oligonucleotide (usually 25- to 70-mers) arraysand gene expression arrays containing PCR products prepared from cDNAs.In forming an array, oligonucleotides can be either prefabricated andspotted to the surface or directly synthesized on to the surface (insilico). For example, Affymetrix's popular GeneChip (Santa Clara,Calif.) are arrays fabricated by direct synthesis of oligonucleotides onthe glass surface. Oligonucleotides, usually 25-mers, are directlysynthesized onto a glass wafer by a combination of semiconductor-basedphotolithography and solid phase chemical synthesis technologies. Eacharray contains up to 900,000 different oligos and each oligo is presentin millions of copies (FIG. 2). Since oligonucleotide probes aresynthesized in known locations on the array, the hybridization patternsand signal intensities can be interpreted in terms of gene identity andrelative expression levels.

Although in principle, microarray experiments have opened a gateway tovast amount of data at a relatively fast speed and low cost, in reality,there still remains a number of key technical issues that limitsmicroarray experiments from reaching their full potential. Inparticular, because interpretation of microarray measurements requirescomputational methods to translate the digital images into correspondingconcentration readings, the accuracy of an microarray experiment largelyhinges on the capability of available image analysis methods toaccurately translate image intensity values to true concentrationvalues. Many factors are known to play a role in this translationprocess, including the physical construction of an array, the chemistryof the sample, and the optics of the array reader, just to name a few.

In general, measurement values obtained from each array will have a‘block effect’ due to variation in RNA extraction, labeling, fluorescentdetection, etc. Without statistical treatment, this block effect isconfounded with real expression differentiation. The process of applyingstatistical treatment to reduce the block effect is defined asnormalization. This process is usually done at the probe level. Severalnormalization methods for oligonucleotide arrays have been proposed andpracticed. One approach uses lowess normalization to correct fornon-central and nonlinear bias observed in M-A plots. Another class ofapproaches correct for the nonlinear bias seen in Q-Q plots. As Workmanet al. and Bolstad et al. discussed in their papers (Workman et al.(2002), Genome Biol., 3, 1-16; Bolstad et al., (2003), Bioinformatics,19, 185-193, the entire contents of both articles are incorporatedherein by reference), several assumptions must hold in the methods usingquantiles. First, most genes are not differentially regulated; second,the number of up-regulated genes roughly equals the number ofdown-regulated genes; third, the above two assumptions hold across thesignal-intensity range. These three assumptions are adopted by mostnormalization methods in use today. For the purpose of discussion, thesethree assumption will herein be referred to as the standard assumptions.

Unfortunately, the standard assumptions do not always hold true. Thus,current crop of normalization methods are all quite restrictive in theircapabilities. Without a reliable and generally applicable method ofnormalizing array data, the validity of results obtained from microarrayexperiments will always require further validation. Therefore, there isstill a need in the art for a better normalization method that aregenerally applicable.

Accordingly, it is one object of the present invention to provideimproved methods for analyzing microarray data that is capable ofhandling experimental conditions beyond the standard assumptions.

It is also an objective of the present invention to provide a betterframework for processing microarray data that integrates normalizationand summarization of data, thereby, improving the efficiency ofmicroarray analysis.

These and other objects of the present invention are achieved throughthe methods and systems of the present invention. The principles andexemplary embodiments of the present invention will now be described indetail below.

SUMMARY OF THE INVENTION

In one aspect, the present invention provides a method of analyzingmicroarray data, comprising the steps of: providing a set of microarraydata; grouping the microarray data into reference data and target data;normalizing the microarray data by applying a least trimmed squaresregression method or a symmetric variant thereof to determine parametersfor a linear model that fits the data; and analyzing the normalizedmicro-array data to obtain a desired result.

In another aspect, the present invention also provides a method foranalyzing microarray data, comprising the steps of: providing a set ofmicroarray data; subdividing the microarray data into subarrays;normalizing the microarray data within each subarray; and analyzing thenormalized data to obtain a desired result.

In yet another aspect, the present invention further provides a methodfor obtaining expression profiles from microarray experiments whichstreamlines normalization and summarization of data, comprising thesteps of: providing a set of microarray data from duplicate microarrayswherein at least one microarray is treated with treatment sample and atleast one microarray is treated with control sample; selecting aplurality of reference arrays from among the microarrays and a pluralityof corresponding target arrays from among the remaining microarraysaccording to a design of the microarray experiment; applying anormalization procedure to each pair of reference and targetmicro-arrays; summarizing the expression value for each probe-set fromnormalized microarray and reference array data according to aprobe-treatment-reference (PTR) model, and estimating the parameters inthe PTR model by a Least Absolute Deviations approach, whereby the stepsof normalization and summarization are streamlined.

In yet another aspect of the present invention, there is provided Amethod for detecting defective areas on a microarray, comprising:dividing the array into a plurality of subarrays; applying anormalization procedure comprising a least trimmed squares method or asymmetric variant thereof, wherein said least trimmed squares regressionmethod or the symmetric variant thereof normalizes the microarray databy estimating parameters for a linear model and fitting the data to themodel; and estimating the parameters of the linear models across theplurality of subarrays to detect subarrays that are defective.

In addition to providing the above mentioned methods, the presentinvention further provides computer systems for practicing the abovementioned methods as well as computer readable media encoding themethods.

Other aspects and advantages of the invention will be apparent from thefollowing description and the appended claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a general workflow diagram for an exemplary microarrayexperiment.

FIG. 2 shows an exemplary Affymetrix-type array. The Affymetrix-typearray (termed GeneChip by Affymetrix) is made up of thousands of tileswith tethered nucleotides (tiles are sometimes, confusingly, calledcells). A single gene is represented by adjacent tiles 16 to 24 times(i.e. each tile has tethered oligonucleotide), depending on the type ofarray (this serves as an internal repeat for each hybridization). Foreach of these tiles (oligonucleotide is a Perfect Match, PM—positiveprobe) there are the same number of adjacent tiles that are Mismatches(MM—negative probe). This therefore makes up a number of probe pairs.This serves as an internal control. The PMs and MMs for a single gene iscollectively termed as a probe set.

FIG. 3 shows the slope matrices of two arrays which illustrate differentspatial patterns in scale. The common reference is Array M. (A) Array Pversus M; (B) Array N versus M. (C and D) Their histograms are shown atbottom correspondingly.

FIG. 4 shows the M-A plots of spike-in data after SUB-SUB normalization:(A) trimming fraction is 0.4; (B) trimming fraction is 0.

FIG. 5 (A-F)M-A plots of perturbed spike-in dataset after SUB-SUBnormalization. The x-axis is the average of log-intensities from twoarrays. The y-axis is their difference after normalization. In the topfour subplots, 20% randomly selected genes have been artificiallyup-regulated by 2.5-fold in Array Q, R, S and T. The differentiatedgenes are marked red, and undifferentiated genes are marked black. Thetrimming fractions in the subplots are: A, 50%; B, 30%; C, 20%; D, 10%.In the two subplots at the bottom, 20% randomly selected genes have beenartificially up-regulated by 1.5-fold in Array Q, R, S and T. Thetrimming fractions are: E, 50%; F, 0%.

FIG. 6 shows a schematic representation of the PTR method.

FIG. 7 Top (A1-A3): invariant-set; middle (B1-B3): quantile; bottom(C1-C3): sub-array. Left column (A1, B1 and C1): the reference isperturbed array Exp03 R1*; Middle column: the reference in both A2 andC2 is array Exp03 R2, while the reference in B2 is the pseudo-referencedefined as the average quantiles of all six arrays; Right column (A3, B3and C3): the PTR method result obtained using all six arrays asreferences. The grey dots are non-spike-in genes; the black dots arespike-in genes which are expected to have log-ratio M=1. We can see thatPTR method results are not affected by the perturbed array Exp03 R1* andoffers the smallest variation for non-spike-in genes.

FIG. 8 These plots compare the PTR method with other pre-processingmethods based on the variation of non-spike-in genes. The PTR methodgives the smallest variation for all three normalization algorithms.

FIG. 9 X-axis: 1—specificity; Y-axis: sensitivity. The PTR methodperforms the best in all cases.

FIG. 10 shows an exemplary computer system according to one embodimentof the present invention.

FIG. 11 This reference effect box plot is get from the PTR model fittingon the perturbed data set after the invariant-set normalization. Thefirst reference array, Exp03 R1*, has been perturbed by adding noise. Itshows a quite different distribution than others.

DETAILED DESCRIPTION

To facilitate a full and complete understanding of the presentinvention, we will first begin with a brief discussion of thetheoretical underpinnings of the methods and systems from whichembodiments of the present invention are derived. However, it will beunderstood that the purpose of this discussion is only for illustration,and not to be interpreted as limiting in any way.

Overview

The problem of normalization can be conceptually understood as the needto compare apples to apples. For example, when comparing images takenfrom two separate arrays, the data from each array are biaseddifferently due to the variability in the physical construction of thearrays and other factors. Thus, direct comparison of signals from thetwo arrays will amount to comparing apples to oranges. To overcome thisproblem, one must scale the signals from the two arrays to a commonscale, or, in the microarray analysis jargon, data from the two arraysmust be normalized before meaningful comparison can be carried out.

As mentioned in the background section, normalization is a majortechnical problem in microarray analysis. Many methods have beenproposed in the art. However, existing methods can only deal withsamples that differ from each other in a limited degree; largedifferences between two samples, especially asymmetric differences arenot adequately addressed by existing methods. The inventors of thepresent invention have now formulated the normalization problem as ablind inversion problem. This formulation has the advantage ofjustifying the normalization results for various scenarios includingthose with little differentiation and those with substantialdifferentiation.

The basic concept of blind inversion is to use the information about thejoint distribution of hybridization levels of the target and referenceto find a transformation that can then be applied to transform theindividual data points from observed values to true values. Twodifferent ideas exist to achieve this goal. First, quantiles allows oneto compare distributions. In this regard, the Q-Q plot is the standardgraphical tool for the purpose. The normalization proposed in Sidorov etal. (Inform. Sci., 146, 67-73 (2002), the entire content of which isincorporated herein by reference), Workman et al. (Genome Biol., 3,1-16, (2002)), and Bolstad et al., (Bioinformatics, 19, 185-193, (2003))aims to match the marginal distribution of hybridization levels from thetarget with that from reference. Although slight and subtle differenceexists between the two principles, quantile methods work well for arrayswith little differentiation. The second idea is regression, eitherlinear or nonlinear (Yang et al., Microarrays: Optical Technologies andInformatics. SPIE Vol. 4266; Schadt et al. Cell. Biochem., 80, 192-202,(2000), the contents of both articles are incorporated herein byreference). The inventors have adopted the regression perspective indevising the methods of the present invention as it is easier to dealwith the situations in which the standard assumptions are violated.

To illustrate exemplary methods of the present invention, we firstconsider the simple case of comparing two duplicate microarrays treatedwith different samples. When the two samples have largely differentexpression profiles, one needs to identify a ‘base’ subset for thepurpose of normalization. This subset should exclude those probescorresponding to differentially expressed genes and abnormal probes dueto experimental variation. Other methods known in the art generallyadopt an ‘invariant set’ approach to choosing the base set. Theinvariant set can be a set of housing keeping genes that are known toexpress at the same level in different samples, or it may be identifiedby a ranking method that selects from the two samples a set of geneshaving the same ranking in their respective array data set. One caneasily see that if the two datasets vary from each other greatly, theinvariant set approach is ill equipped to handle such situations.

In the present invention, we propose a new approach to theidentification of the base set and estimation of the transformation in asimultaneous fashion by adapting the least trimmed squares (LTS)algorithm (Rousseeuw, P. J. and Leroy, A. M. (1987) Robust Regressionand Outlier Detection. Wiley, New York, the entire content of which isincorporated herein by reference). In this new approach, substantialdifferentiation is accommodated in LTS by setting an appropriatetrimming fraction.

Another variability that may influence array normalization is theuncontrolled spatial variations in the arrays introduced duringmanufacturing or other random processes. There may also bearray-specific spatial patterns due to uneven hybridization andmeasurement process. For example, reagent flow during the washingprocedure after hybridization may be uneven; scanning may benon-uniform. We have observed different spatial patterns from one arrayto another. This problem is not well-recognized in the art. In thepresent invention, we explicitly take this spatial bias intoconsideration by divide each array into subarrays that consist of a fewhundred probes and normalize probe intensities within each subarray.Other spatial normalization, such as that disclosed in Workman et al.(Genome Biol., 3, 1-16. (2002)) only considers the spatial effect inbackground. In comparison, methods of the present invention are capableof adjusting for spatial differences both in background and in scale.

We now turn to the detailed conceptual formulation of the presentinvention.

Statistical Principle of Normalization

To illustrate the statistical principle underlying normalization, weconsider the simple case of two arrays: one reference and one target.Denote the measured fluorescence intensities from the target andreference arrays by (U_(j),V_(j)). Denote true concentrations ofspecific binding molecules by (Ū_(j), V _(j)). Ideally, we expect that(U_(j),V_(j))=(Ū_(j), V _(j)). In practice, measurement bias exists dueto uncontrolled factors and we need a normalization procedure to adjustmeasurement. Next, we have another look at normalization. Consider asystem with (Ū_(j), V _(j)) as input and (U_(j),V_(j)) as output. Leth=(h₁, h₂) be the system function that accounts for all uncontrolledbiological and instrumental bias; namely,

$\quad\left\{ \begin{matrix}{U_{j} = {{h_{1}\left( {\overset{\sim}{U}}_{j} \right)}.}} \\{V_{j} = {{h_{2}\left( {\overset{\sim}{V}}_{j} \right)}.}}\end{matrix} \right.$

The goal is to reconstruct the input variables (Ū_(j), V _(j)) based onthe output variables (U_(j),V_(j)). Thus, in the present invention, thenormalization problem is envisioned as a blind inversion problem, inwhich both input values and the effective system are unknown. Asdescribed above, the general idea of blind inversion is to find atransformation that matches the distributions of input and output. To dothis, we must determine the joint distribution of true concentrations(Ū_(j), V _(j)). First, let us assume that the target and referencearray are biologically undifferentiated. Under such condition, thedifferences between the target and reference are purely caused by randomvariation and uncontrolled factors. In this ideal case, it is reasonableto assume that the random variables {(Ū_(j), V _(j)), j=1, . . . } areindependent samples from a joint distribution {tilde over (Ψ)} whosedensity centers around the straight line Ū= V, namely, E( V|Ū)=Ū. Theaverage deviations from the straight line measure the accuracy of theexperiment. If the effective measurement system ĥ is not an identityone, then the distribution of the output, denoted by Ψ, could bedifferent from {tilde over (Ψ)}. An appropriate estimate ĥ of thetransformation should satisfy the following: the distribution ĥ⁻¹(Ψ)matches {tilde over (Ψ)}, which centers around the line V=Ū. In otherwords, the right transformation straightens out the distribution of Ψ.

Next we consider the estimation problem. Roughly speaking, only thecomponent of h₁ relative to h₂ is estimable. Thus we let v=h₂( v)= v. Inaddition, we assume that h₁ is a monotone function. Denote the inverseof h₁ by g, then we expect the following is valid.

Ē( V|Ū)= U or E( V|g(U))=g(U)

PROPOSITION 1: Suppose the above equation is valid, then g is theminimizer of min_(l) E(V−l(U))².

According to the well-known fact of conditional expectation, E(V|g(U))=g(U) minimizes E(V−l₁(g(U))² with respect to l₁. Next writel₁(g(U))=l(U). This fact suggests that we estimate g by minimizing

$\sum\limits_{j}{\left( {V_{j} - {g\left( {U_{j} - 1} \right)}} \right)^{2}.}$

When necessary, we can impose smoothness on g by appropriate parametricor non-parametric forms.

Differentiation Fraction and Undifferentiated Probe Set

Next we consider a more complicated situation. Suppose that a proportionλ of all the genes are differentially expressed while other genes arenot except for random fluctuations. Consequently, the distribution ofthe input is a mixture of two components. One component consists ofthose undifferentiated genes, and its distribution is similar to {tildeover (Ψ)}. The other component consists of the differentially expressedgenes and is denoted by

. Although it is difficult to know the form of

a priori, its contribution to the input is at most λ. The distributionof the input variables (Ū_(j), V _(j)) is the mixture (1−λ){tilde over(Ψ)}+λ

. Under the system function h, {tilde over (Ψ)} and

are transformed respectively into distributions denoted by Ψ and

, i.e. Ψ=h({tilde over (Ψ)}),

=h(

). This implies that the distribution of the output (U_(j),V_(j)) is(1−λ) Ψ+λ

. If we can separate the two components Ψ and

, then the transformation h of some specific form could be estimatedfrom the knowledge of {tilde over (Ψ)} and Ψ.

Spatial Pattern and Sub-arrays

In the present invention, it is envisioned that normalization can becarried out in combination with a stratification strategy. For cDNAarrays, researchers have proposed to group spots according to the layoutof array-printing so that data within each group share a more similarbias pattern. And then normalization is applied to each group. This isreferred to as within-print-tip-group normalization. On a high-densityoligonucleotide array, tens of thousands of probes are laid out on achip. To take into account any plausible spatial variation in h, wedivide each chip into sub-arrays, or small squares, and carry outnormalization for probes within each subarray. To get over any boundaryeffect, we allow subarrays to overlap. A probe in overlapping regionsgets multiple adjusted values from subarrays it belongs to, and we taketheir average.

Parameterization

Since each subarray contains only a few hundred probes, we choose toparameterize the function g by a simple linear function α+βu, in whichthe background α and scale β represent uncontrolled additive andmultiplicative effects, respectively.

Simple Least Trimmed Squares

Our target solution consists of two parts: (i) identify the ‘base’subset of probes; (ii) estimate the parameters in the linear model. Weadopt LTS to solve the problem. Starting with a trimming fraction ρ, seth=[n(1−ρ)]+1. For any (α,β), define r(α,β)_(i)=v_(i)−(α+βu_(i)); LetH_((α,β)) be a size-h index set that satisfies the following property:|r(α,β)_(i)|≦|r(α,β)_(j)|, for any iεH_((α,β)) and j≠H_((α,β)). Then theLTS estimate minimizes

$\sum\limits_{i \in H_{({\alpha,\beta})}}{r\left( {\alpha,\beta} \right)}_{i}^{2}$

The solution of LTS can be characterized by either the parameter (α,β)or the size-h index set H. It is this dual form that we find it idealfor our purpose. Statistically, LTS is a robust solution for regressionproblems. It has the advantage of being able to achieve any givenbreakdown value by setting a proper trimming fraction. It also has√{square root over (n)}-consistency and asymptotic normality under someconditions. In addition, the LTS estimator is regression, scale, andaffine equivariant.

An LTS solution naturally associates with a size-h index set. By settinga proper trimming fraction r, we expect the corresponding size-h set isa subset of the undifferentiated probes explained earlier. Obviously,the trimming fraction r should be larger than the differentiationfraction p.

Multiple Arrays and Multiple References

In the case of multiple arrays, the strategy of normalization hinges onthe selection of reference. In some experiments, a master reference canbe defined. For example, the time zero array can be set as a referencein a time course experiment. In experiments of comparing tumor andnormal tissues, the normal sample can serve as a reference. In othercases, the median array or mean array are options for references.Another strategy is: first, randomly choose two arrays, one referenceand one target, for normalization; use the normalized target array fromthe last normalization as the reference for the next normalization;iterate this procedure until all arrays have been normalized once; andrepeat this loop for several runs. Prior art methods for summarizingmultiple array experiments include the well-known median polishingalgorithm in the RMA method (Irizarry et al., Biostatistics, 4, 249-264,(2003), the entire content of which is incorporated by reference). Thequantile normalization method used in RMA can only deal with sample withlittle differentiation, and only use one reference, either a raw arrayor one synthesized from raw arrays. In the present invention, we furtherpropose a method of summarizing multiple array experiments, the detailsof which are described in the next section.

The Probe-Treatment-Reference (PTR) Summarization Model

Thus far, we have established that the estimation of gene expressionfrom probe intensities can be envisioned as a statistical problem.Current methods such as the method implemented in Affymetrix's MAS 5.0software, the dChip software, and the RMA software all attempt to solvethis problem by providing software consisting of two separate modules:one for normalization and one for summarization of data. Normalizationaims to balance intensity values in order to reduce non-biologicalvariations which are introduced during sample preparation andinstrumental reading. Summarization combines normalized signal values ineach probe-set and produces a final abundance estimate for thecorresponding gene represented by the probe-set.

Normalization requires the specifications of reference and targetarrays. One can normalize target arrays against a reference, no matterwhether it is a raw microarray or an artificially-defined dataset. Inthe invariant-set normalization method, which is a part of the dChipsoftware, the median intensity of each array is calculated, and thearray with the median of these overall medians is chosen as thereference; however, other options are also allowed. The normalization iscarried out according to the smooth curve fitted from the rank-invariantintensity set between the reference and target array. The quantilenormalization in RMA uses complete data information and defines apseudo-reference by the averaged quantiles. The normalization is carriedout based on the quantile-quantile transformation. In the subarraynormalization method of the present invention, once a reference and atarget are given, it divides the whole array into sub-windows andnormalizes probe intensities within each window using least trimmedsquares (LTS) regression method. However, the issue of referenceselection has not been well addressed.

In this invention, we propose a Probe-Treatment-Reference (PTR) method,which takes the reference-effect into account. The PTR method aims tostreamline normalization and summarization by allowing multiplereferences. Instead of one reference array, it uses a reference set todo microarray pre-processing, namely, every array in this set serves asa reference for normalization. Compared to the two-factor model in theRAA, which contains probe- and array-specific effect (later we refer toit as the PA model), we reformulate the array-specific factor by atreatment factor and add a reference factor in the PTR model. In oneexemplary embodiment, we implement the model by the least absolutedeviations (LAD) approach, which has the advantage of being robust inthe sense of the bounded influence (Bloomfield et al., Least absolutedeviations: theory, applications, and algorithms. Birkhauser 1983, therelevant portion of which is incorporated herein by reference).

The proposed PTR method is capable to integrate normalization withsummarization in a unified framework. It can be applied to severalexisting normalization methods, and is particularly useful for thesub-array normalization which aims to reduce spatial variation. Becausethe reference-specific effect is adjusted at the probe-set level,implicitly, from the reference set, our model will define a “reference”for each probe-set, which may not come from the same raw array. Themethod has the advantage that the fold change estimates are resistant toa bad reference array. It reduces the variation of non-differentiallyexpressed genes and thereby increases the detection power ofdifferentially expressed genes.

The scheme of the PTR method is shown in FIG. 6. The PTR model fittingon is carried out on each probe-set. The inputs of the fitting arenormalized results using multiple references. For the purpose of thisdiscussion, we note that only PM probes are used even if the MM probesare available. Let variable y_(ijkl) be the j^(th) normalized probeintensity value of the l^(th) replicate for the i^(th) treatment,against the k^(th) reference array, where i=1 . . . , I; j=1, . . . J;k=1, . . . , K; l=1, . . . , L. We postulate that log₂(y_(ijkl)) followsthe three-factor model as below:

log₂(y _(ijkl))=μ+α_(i)+β_(j)+γ_(k)+ε_(ijkl),

where μ is the global term; α_(i) represents the i^(th) treatment; β_(j)represents the j^(th) probe-specific effect; and γ_(k) represents thek^(th) reference-specific effect. It is neither simple nor obvious tospecify the distribution form for ε_(ijkl). In addition, they arecorrelated. In order to make the model identifiable, we can impose oneof the following constraints:

-   -   Sum constraints:

${{\sum\limits_{i}\alpha_{i}} = 0},{{\sum\limits_{j}\beta_{j}} = 0},{{{\sum\limits_{k}\gamma_{k}} = 0};}$

-   -   Median constraints:        median({α_(i)})=0,median({β_(j)})=0,median({γ_(k)})=0

We use μ+α_(i) for the final transcript abundance estimate for thei^(th) treatment.

Suppose that we have two treatments and each has three replicates. Thetwo-factor model has 22 (1+5+10) parameters, assuming the probe-set has11 PM probes. After the model fitting, the expression value for eachtreatment usually will be calculated using the medians or means acrossthe three replicates. The PTR model has 23 (1+1+10+5) parameters, if weinclude all six arrays in the reference set. The expression values foreach treatment are calculated directly. Meanwhile, it does notnecessarily lead to over-fitting if we use more reference arrays, sincethe number of normalized array increases accordingly. For example, usingthe cross strategy, three references generate 132 (4×11×3) normalized PMintensity values, while six references generate 264 (4×11×6) values.

Least Absolute Deviations (LAD) Estimation and its Computation

As described above, we have demonstrated an exemplary embodiment of thePTR model with LAD estimator implementation for estimating theparameters in the PTR model. That is, we minimize the sum of absoluteerrors (SAE):

${S\; A\; E} = {{\sum\limits_{i,j,k,l}{ɛ_{ijkl}}} = {\sum\limits_{i,j,k,l}{{{{\log_{2}\left( y_{ijkl} \right)} - \mu - \alpha_{i} - \beta_{j} - \gamma_{k}}}.}}}$

The LAD problem can be reformulated as a linear programming (LP) problemand thereby be solved via LP algorithms, such as the simplex and theinterior point algorithm. However, in the PTR model, we notice that allregressors are categorical variables. It is easily seen that SAE is notminimized if the median of residuals indexed by the same level of anyfactor is not zero. in this case the corresponding α_(i), β_(j) or γ_(k)can be adjusted to make the median be zero and reduce the sum in thethree-factor model equation. Therefore, the LAD solution has theproperty:

$\quad\left\{ \begin{matrix}{{{{median}\left( {\left\{ ɛ_{ijkl} \right\} i} \right)} = 0},} \\{{{{median}\left( {\left\{ ɛ_{ijkl} \right\} j} \right)} = 0},} \\{{{median}\left( {\left\{ ɛ_{ijkl} \right\} k} \right)} = 0.}\end{matrix} \right.$

Consequently, we can minimize the sum of absolute deviations by “medianpolish” approach. Namely, in each step, we sweep out the median for eachlevel of one categorical variable. In each iteration, we run the medianpolishing through all categorical variables. The SAE is reduced duringeach step and we stop the iteration once it becomes stable. Ourexperiences show that at most 20 iterations give satisfactory results.

Strategy of Normalization and Summarization

To further illustrate the PTR method we describe here a typicaltreatment-control case where we have three replicates for control andthree for treatment. First, we select multiple references and theirtarget arrays. We propose two simple and straightforward strategies asfollows.

-   -   The all-pairwise strategy: all arrays are included in the        reference set; for each reference, all the other arrays are its        targets.    -   The cross strategy: all arrays are included in the reference        set; for each reference from control, we take replicates from        treatment as its target arrays; conversely, for each reference        from treatment, we take replicates from control as its target        arrays.

Second, we may use existing normalization algorithms such as theinvariant-set, sub-array and quantile, to do normalization between eachreference and its target arrays. In one exemplary embodiment, we use thefunction normalize.AffyBatch.invariantset in the BioConductor's affypackage to carry out the invariant-set normalization. We keep thedefault parameter settings but allow the reference to be selectedmanually. We also applied normalization method of the present inventionfor sub-array normalization. The window size is 25, the overlapping sizeis 10 and the trimming factor is 0.55 for the HG-U133A dataset. We maynormalize each target array against a raw reference array as follows:sort the reference and the target array respectively in the ascendingorder; replace the sorted intensity values in each target array withthose in the reference array; rearrange intensities in each target arrayto the original order.

Finally, for each probe-set, we summarize the arrays fromlog-transformed PM intensities according the three-factor PTR model:log₂ (Intensity)=global term+treatment effect+probe effect+referenceeffect. The model states that the variation of logarithmic probe signalvalues could be sufficiently explained by treatments, probe affinitiesand references in normalization. The global term and treatment effectsare taken to be the final transcript abundance estimates; the referenceeffect and the probe effect could be used for diagnosis.

EXEMPLARY EMBODIMENTS

Having the benefit the above theoretical discussion, we now turn ourattention to the exemplary embodiments of the present invention.

In one aspect, the present invention provides a method of analyzingmicroarray data, comprising the steps of: providing a set of microarraydata; grouping the microarray data into reference data and target data;normalizing the microarray data by applying a least trimmed squaresregression method or a symmetric variant thereof to determine parametersfor a linear model that fits the data; and analyzing the normalizedmicro-array data to obtain a desired result.

In general, a person skilled in the relevant art will appreciate that amethod according to the present invention is not limited to the analysisof microarray data, but is also applicable to any data analysissituations where normalization of replica dataset is required. For thepurpose of discussion, analysis of microarrays are provided as exemplaryembodiments.

The term “microarray” as used herein refers to a broad range ofinstrumentation and techniques that share the same characteristics ofhaving a miniature footprint, and capable of a high degree ofparallelism for high-throughput data generation. Exemplary microarraysinclude, but are not limited to oligonucleotide arrays (also known asAffymetrix-type arrays), cDNA arrays, bead arrays, pathway arrays,ChIP-chip experiments, methylation arrays, exon arrays, tissue arrays,and protein arrays.

In embodiments of the present invention, normalization is done usingregressional analysis, preferably a least trimmed squares regressionmethod or a symmetric variant thereof. Computation of least trimmedsquares algorithm may be implemented by any means commonly known in theart. Preferably, a fast and stable computation algorithm computationpreviously introduced by the inventors is used (Li, L. M., Comput. Stat.Data Anal., 48, 717-734, (2004), the entire content of which isincorporated herein by reference).

When analyzing data obtained from oligonucleotide arrays, methods of thepresent invention may further include the step of dividing the arrayinto subarrays and normalizing the data within each subarray. Typically,all data from the probe-set are used, but alternatives such as excludingdata from the mismatched probes may also be advantageous considered. Thesubarray may range from about 10×10 data points in size to about 100×100data points. Adjacent subarrays may also be allowed to overlap eachother. The portion of overlap may range from about 0% to any percentageless than 100%.

Often times, design of microarray experiment will call for duplicates.Hence, in some embodiments, methods of the present invention will takemicroarray data from a set of duplicate microarrays wherein at least oneof the duplicate microarrays is treated with a reference sample and atleast one of the duplicate microarrays is treated with a target sample.

One major advantage of normalizing data with a least trimmed squaresmethod according to embodiments of the present invention is that one mayset the trim fraction in accordance with the desired sensitivity andexperimental design. The trim faction is preferably larger than thefraction of differentiated probes. This is important because thefraction used in regression should be within the fraction range ofundifferentiated probes.

The concept of sub-dividing an array into subarrays for analysis is auseful tool in the analysis of data that are arranged in matrix format.Thus, in another aspect, the present invention can also be seen asproviding a method for analyzing microarray data, comprising the stepsof: providing a set of microarray data; subdividing the microarray datainto subarrays; normalizing the microarray data within each subarray;and analyzing the normalized data to obtain a desired result A skilledperson in the art will readily appreciate that the concept of subarraywill also work with normalization techniques other than the leasttrimmed squares regression. However, the use of least trimmed squaresregression is preferred.

After the array data are normalized, one may then proceed to analyze thedata to obtain the desired outcome. Exemplary desired outcome mayinclude time-series of gene expression profile, or any other informationrelevant to answering a biological question. Analysis and interpretationof the normalize array data will generally be determined by experimentaldesign. To deal with the large number of data points generated, a numberof statistic methods may be beneficially employed, which may include,but are not limited to estimation, testing, clustering, anddiscrimination.

In yet another aspect, the present invention further provides a methodfor obtaining expression profiles from microarray experiments whichstreamlines normalization and summarization of data, comprising thesteps of: providing a set of microarray data from duplicate microarrayswherein at least one microarray is treated with treatment sample and atleast one microarray is treated with control sample; selecting aplurality of reference arrays from among the microarrays and a pluralityof corresponding target arrays from among the remaining microarraysaccording to a design of the microarray experiment; applying anormalization procedure to each pair of reference and targetmicro-arrays; summarizing the expression value for each probe-set fromnormalized microarray and reference array data according to aprobe-treatment-reference (PTR) model, and estimating the parameters inthe PTR model by a Least Absolute Deviations approach, whereby the stepsof normalization and summarization are streamlined.

The arrays may be treated at multiple levels, or treated at a singlelevel. In either case, the method is capable of accommodating bothexperimental designs.

In the PTR method, the key is the use of multiple references. In oneembodiment, a reference selection strategy is adopted such that allmicroarrays are included in the reference set; and, for each reference,all the other microarrays are its targets. In another embodiment,reference and target arrays are selected such that all microarraystreated with control sample are included in the reference set, and foreach reference that is treated with control sample, replicates fromarrays treated with treatment sample are taken as its target arrays.

In yet another aspect of the present invention, there is provided amethod for detecting defective areas on a microarray, comprising:dividing the array into a plurality of subarrays; applying anormalization procedure comprising a least trimmed squares method or asymmetric variant thereof, wherein said least trimmed squares regressionmethod or the symmetric variant thereof normalizes the microarray databy estimating parameters for a linear model and fitting the data to themodel; and estimating the parameters of the linear models across theplurality of subarrays to detect subarrays that are defective.

In addition to providing the above mentioned methods, the presentinvention further provides computer systems for practicing the abovementioned methods as well as computer readable media encoding themethods.

In one embodiment, it is envisioned that the method is implemented to beexecuted by a computer as a stand-alone workstation. Computerimplementation of the method may be achieve by any commonly usedprogramming methodologies known in the art. Exemplary implementationsmay include C/C++, Fortran, Java, or the like. It is also envisionedthat a microarray reader system may incorporate a computer systemaccording to the present invention. In such a scenario, customizedhardware and circuitry may be created to execute methods of the presentinvention at an increased speed than general purpose PC. Incorporatingcomputer system of the present invention into a microarray reader systemprovides the advantage of convenience to the user. FIG. 10 shows anexemplary computer system of the present invention.

Other approaches of implementing the methods of the present inventionare also contemplated. For example, a web-based application servicemodel wherein instruction for directing a computer to execute the methodis delivered in real-time over the network offer certain advantages andis contemplated in the present invention.

To further illustrate the methods and systems of the present invention,the following specific examples are provided.

EXAMPLES Example 1 Microarray Data

The Affymetrix Spike-in dataset, which includes 14 arrays, was obtainedfrom Affymetrix HG-U95 chips. Fourteen genes in these arrays werespiked-in at given concentrations in a cyclic fashion known as a Latinsquare design. The data are available from Affymetrix's website(http://www.affymetrix.com/support/technicallsample_data/datasets.affi).In the examples described herein, eight arrays were chosen from thecomplete set and split into two groups. The first group contained fourarrays: m99hpp_av06, 1521n99hpp_av06, 1521o99hpp_av06 and1521p99hpp_av06. The second group contained four arrays: q99hpp_av06,1521r99hpp_av06, 1521s99hpp_av06 and 1521t99hpp_av06. For the sake ofbrevity, these arrays will henceforth be designated by letters M, N, O,P, Q, R, S, and T. As a result, the concentrations of 13 spiked-in genesin the second group are 2-fold lower. The concentrations of theremaining spike-in genes are respectively 0 and 1024 in the two groups.In addition, two other genes are so controlled that their concentrationsare also 2-fold lower in the second group compared with the first one.

From the same Affymetrix webpage, two replicates using yeast arrayYG-S98 were also available: Yeast-2-121501 and Yeast-2-121502. Thesedata were used to study the variation between array replicates.

Expression profiles offer a way to study the difference between humansand their closest evolutionary relatives. We consider the publiclyavailable dataset fromhttp://email.eva.mpg.de/˜khaitovi/supplement1.html (Enard et al.,Science, 296, 340-343, (2002), the entire content of which isincorporated herein by reference). Two brain samples were extracted fromeach of three humans, three chimpanzee and one orangutan. In whatfollows we only show results on two human individuals, HUMAN 1 and HUMAN2, one chimpanzee, CHIMP. 1 and the orangutan, ORANG. The mRNAexpression levels were measured by hybridizing them with the Affymetrixhuman chip HG-U95.

Implementation and SUB-SUB Normalization

We have developed a module to implement the normalization methoddescribed above, referred as SUB-SUB normalization. The core code iswritten in C, and we have interfaces with Bioconductor in R. The inputof this program is a set of Affymetrix CEL files and outputs are theirCEL files after normalization. Three parameters need to be specified:subarray size, overlapping size and trimming fraction. The sub-arraysize specified the size of the sliding window. The overlapping sizecontrols the smoothness of window-sliding. Trimming fraction specifiesthe breakdown value in LTS. An experiment with an expected higherdifferentiation fraction should be normalized with a higher trimmingfraction.

Parameter Selection

We have tried many combinations of the three parameters on severaldatasets. In some reasonable range, the interaction between theparameters is negligible. In general, the smaller the sub-array size is,the more accurately we can capture spatial bias while the less number ofprobes are left for estimation. Thus, we need to trade off bias andvariation. From our experiments, we recommend 20·20 for AffymetrixHG-U95 and HG-U133 chips. The value of overlapping size is the same forboth directions, and we found its effect on normalization is the leastamong the three parameters. Our recommendation is half of the sub-arraysize. For example, it is 10 if sub-array size is 20·20. According to ourexperience, it can even be set to 0 (no overlapping between adjacentsub-arrays) to speed up computation without obvious change tonormalization. The selection of trimming fraction should depend onsamples to be compared in the experiments and quality of microarraydata. For an experiment with 20% differentiated genes, we should set atrimming fraction >20%. Again we need a trade off between robustness andaccuracy in the selection of trimming fraction. On the one hand, toavoid breakdown of LTS, we prefer large trimming fractions. On the otherhand, we want to keep as many probes as possible to achieve accurateestimates of a and b. Without any a priori, we can try differenttrimming fractions and look for a stable solution. Our recommendationfor starting value is 50%.

Affymetrix Spike-in Dataset

We first investigate the existence of spatial pattern. The HGU95 chiphas 640×640 spots on each array. We divided each array into sub-arraysof size 20×20. We run simple LTS regression on the target with respectto the reference for each sub-array. This results in an intercept matrixand a slope matrix of size 32·32, representing the spatial differencebetween target and reference in background and scale. We first takeArray M as the common reference. The slope matrices of Array P and M areshown in FIGS. 3A and B, respectively, and their histograms are shown inFIGS. 3C and D. Two quite different patterns are observed. Similarphenomenon. exists in patterns of α. The key observation is that spatialpatterns are array-specific and unpredictable to a great extent. Thisjustifies the need of adaptive normalization.

We carry out SUB-SUB normalization to each of the eight arrays usingArray M as the reference. We experimented with different sub-arraysizes, overlapping sizes and trimming fractions. FIG. 4 shows the M-Aplots summarized from the eight arrays after normalization, namely, thelog-ratios of expressions between the two groups versus the abundance.The sub-array size is 20·20, the overlapping size is 10 and the trimmingfactor are 0.4 and 0 in the subplots FIGS. 4A and B, respectively. Ourresult indicates that both the sub-array size (data not shown) andtrimming fraction matter substantially for normalization. In otherwords, stratification by spatial neighborhood and selection of breakdownvalue in LTS do contribute a great deal to normalization. Overlappingsize has a little contribution in this dataset. Our method identifies 14of the 16 differentially expressed spike-in gene with only a few falsepositives (FIG. 4A).

Perturbed Spike-in Dataset

SUB-SUB normalization protects substantial differentiation by selectingan appropriate trimming fraction in LTS. To test this, we generate anartificial dataset with relatively large fraction of differentiation byperturbing the HG-U95 spike-in dataset. Namely, we randomly choose 20%genes and increase their corresponding probe intensities by 2.5-fold inthe four arrays in the second group. We then run SUB-SUB normalizationon the perturbed dataset with various trimming fractions. The resultsare shown in FIG. 3A, B, C, D for four trimming fractions, 50, 30, 20and 10%. The normalization is satisfactory when the trimming fractionis >30%, or 10% larger than the nominal differentiation fraction. Theextra fraction may account for random variation. In another case, werandomly choose 20% genes and increase their corresponding probeintensities by 1.5-fold. The results corresponding to the trimmingfraction 50 and 0% are shown in FIGS. 3E and F respectively. We notethat the black dots are blocked by red ones in these two subplots whenthey overlap.

Primate Brain Expression Dataset

Compared with other primate brains, such as chimpanzee and orangutan, arelatively high percentage of genes are differentially expressed inhuman brains, and most of them are upregulated in human brains (19,20).Moreover, the chimpanzee and orangutan samples are hybridized with humanHG-U95 chips, so it is reasonable to assume if there were anymeasurement bias in primate mRNA expressions compared with humans, itwould be a downward bias. FIG. 4A-D shows the density functions oflog-ratios of gene expressions for four cases: HUMAN 1 versus ORANG.;HUMAN 2 versus ORANG.; HUMAN 1 versus CHIMP. 1; HUMAN 1 versus HUMAN 2.The results from SUB-SUB (trimming fraction is 20%) and quantilenormalization are plotted in red and blue, respectively. When comparinghumans with primates, the distribution resulted from the SUB-SUB methodis to the right of that resulted from the quantile method. This is moreobvious in the cases of humans versus orangutan, which are moregenetically distant from each other than other cases do; see FIGS. 4Eand F. As expected, the distributions skew to the right and the longtails on the right might have a strong influence on the quantilenormalization, which aims to match marginal distributions from humansand primates in a global fashion. However, in the cases of HUMAN 1versus ORANG. and HUMAN 2 versus ORANG., the modes corresponding to thequantile method are in the negative territory while the modescorresponding to SUB-SUB method are closer to zero. The results fromSUB-SUB normalization seem to be more reasonable. Furthermore, thedifference in the case of HUMAN 1 versus HUMAN 2 is more distinct thanthat in the case of HUMAN 1 versus CHIMP. 1; see the two subplots at thebottom. The analysis in (17) also indicates that HUMAN 2 differs morefrom other human samples than the latter differ from the chimpanzeesamples. We checked the M-A plot of HUMAN2 versus ORANG after SUB-SUBnormalization (figure not shown) and observed that HUMAN 2 has moreup-regulated genes than down-regulated genes compared with ORANG.

Variation Reduction by Sub-Array Normalization

Stratification is a statistical technique to reduce variation. Subarraynormalization can be regarded as a way of stratification. We normalizethe yeast array 2-121502 versus 2-121501 by various normalizationmethods available from Bioconductor. Since the two arrays arereplicates, the difference between them is due to experimentalvariation. In the resulting M-A plots, we fit lowess curves to theabsolute values of M, or |M|. These curves measure the variation betweenthe two arrays after normalization (see FIG. 5). The sub-arraynormalization achieves the minimal variation. As variation is reduced,signal-to-noise ratio is enhanced and power of significance tests isincreased.

Other normalization procedures can be applied at the sub-array level aswell. For example, if differentiation is not substantial, we can applyquantile, lowess, qspline normalization, etc. We note that differentstatistical methods, especially those non-parametric ones, may havespecific requirements on the sample size. To achieve statisticaleffectiveness, we need to select the size of sub-array for eachnormalization method.

Discussion External Controls

In cDNA arrays, some designs use external RNA controls to monitor globalmessenger RNA changes. In our view, external RNA controls play the roleof undifferentiated probe sets. To carry out local normalization, weneed quite some number of external controls for each subgrid. In currentAffymetrix arrays, this is not available. In the Affymetrix yeast2.0arrays, probes for budding yeast, fission yeast, and some bacteria genessuch as from E. coli are included. If the biological samples are frombudding yeast, then we take probes from other organisms such as fissionyeast and bacteria as controls. In normalization methods of the presentinvention, some embodiments may take only external control probes ifthey are available.

In many microarray experiments, our primary goal is the identificationof differentially expressed genes. But the degree of differentiation maybe quite different from one case to another. Next, we briefly mentionsome cases in which a large fraction of genes may be differentiallyexpressed between two samples. First, in one study of the life span ofyeast, we compare expression profiles of a wild-type strain withanother, such as sch9D. The metabolism in the knock-out strain isgreatly reduced and this leads to life span extension. Second, genechips for some organisms are not available. Cross-species hybridizationis a useful strategy for comparative functional genomics. The comparisonof brain expressions of humans versus primates discussed earlier is onesuch example. Third, some customized arrays are so designed that onlyprobes of hundreds of genes relating to a specific biological pathwayare included for the consideration of cost. SUB-SUB normalization usesLTS to identify a ‘base’ subset of probes for adjusting difference inbackground and scale. In theory, the method can be applied to microarrayexperiments with differentiation fractions as high as 50%. In addition,our method does not assume an equal percentage of up- and down-regulatedgenes. In the mean time, LTS keeps the statistical efficiency advantageof least squares.

Nonlinear Array Transformation Versus Linear Sub-array Transformation

To eliminate the nonlinear phenomenon seen in M-A plots or Q-Q plots,methods such as lowess, qspline and quantile normalization use nonlineartransformation at the global level (6,7,22). In comparison, we apply alocal strategy in SUBSUB normalization. One array is split intosub-arrays and a simple linear transformation is fitted for eachsub-array. With an appropriate sub-array size and trimming fraction, thenonlinear feature observed in M-A plots is effectively removed by linearsub-array transformation to a great extent. We hypothesize that thenonlinear phenomenon is partially caused by spatial variation. Onesimulation study also supports this hypothesis, but furtherinvestigation is required. Next, we give one remark regardingnonlinearity. In normalization, we adjust the intensities of a targetarray compared with those of a reference. Even though the dye effect isa nonlinear function of spot intensities, we show that a lineartransformation is a good approximation as long as the majority of probeintensities from the target and reference are in the same range and thushave similar nonlinear effect. Occasionally when the amount of mRNA fromtwo arrays is too different, slight nonlinear pattern is observed evenafter sub-array normalization. To fix the problem, we can apply globallowess after the sub-array normalization. Alternatively, to protectsubstantial differentiation, we can apply a global LTS normalizationsubject to a differentiation fraction once more.

Transformation

The variance stabilization technique was proposed in relation tonormalization. We have tested SUB-SUB normalization on the log-scale ofprobe intensities, but the result is not as good as that obtained on theoriginal scale. After normalization, a summarization procedure reportsexpression levels from probe intensities. we have tried the medianpolishing method (18) on the log-scale. Alternatively, we can do asimilar job on the original scale using Model Based Expression Indexes(MBEI).

Usage of MM Probes

Some studies suggested using PM probes only in Affymetrix chips. Wechecked the contribution of MM probes and PM probes to the subsetsassociated with LTS regressions from all subarrays. FIG. 7 shows thedistribution of the percentage of MM probes in the subsets identified byLTS. Our result shows that MM probes contribute slightly more than PMprobes in LTS regression, mostly in the range 46-56%.

Diagnosis

The detection of bad arrays is a practical problem in the routine dataanalysis of microarrays. In comparison with the obvious physicaldamages, such as bubbles and scratches, subtle abnormalities inhybridization, washing and optical noise are more difficult to detect.By checking values of a and b in LTS across sub-arrays, we can detectbad areas in an array and save information from the rest areas.Consequently, we can report partial hybridization result instead ofthrowing away an entire array.

Example 2 Microarray Data Sets

The Affymetrix HG-U133A data set contains triplicate of 14 experimentswith 42 spike-in genes. These spike-in genes are organized into 14 genegroups, each of which contains 3 genes of the same concentration. Theconcentrations range from 0-512 μM according to a 14×14 Latin squaredesign.

We analyze experiment 3 and 4 particularly. Experiment 3 containstriplicate: Exp03_R1, Exp03_R2 and Exp03_R3; experiment 4 containstriplecate: Exp04_R1, Exp04_R2 and Exp04_R3. The concentrations of 36spike-in genes in experiment 4 are two-fold higher; the concentrationsof the remaining 6 spike-in genes are 0 in either experiment 3 or 4.Later we refer to these six arrays as data set “Expt-3-4”. Besides, wegenerate a perturbed data set by adding noise to array Exp03_R1 andkeeping the other five arrays unchanged. The noise value is defined byδ_(i)=max(0,x_(i)), where x_(i) is a normally distributed randomvariable with a zero mean and variance equal to that of the arrayExp03_R1. We denote this perturbed array by Exp03_R1.

We use another data set, the “Golden spike” data set of Choe et al. in2005, to assess the detection power of differentially expressed genes.The data set contains six Affymetrix DrosGenomel chips, including threereplicates for control and three for treatment. A total of 1309 genesare differentially expressed with pre-defined fold changes from the set,{1.2,1.5,1.7,2.0,2.5,3.0,3.5,4.0}, between the treatment and control.

Perturbed Data Set

Because the PTR method uses multiple references and the robust LADimplementation, we expect that the expression estimates are resistant toa single bad reference array. In FIG. 7, we show the M-A plots of theperturbed data set using different combinations of normalization andreference selections. In these M-A plots, M values are the log-ratios ofexperiment 4 versus experiment 3 for all probe-sets and the A values arethe average log-intensities of the two experiments.

The top, middle, and bottom rows show the results from theinvariant-set, quantile, and sub-array normalization respectively. InA1-B1-C1, we take the perturbed array Ep03_R1* as the reference; inA2-C2, we take the array Exp03_R2 as the reference, while in B2, we takethe average quantiles as the pseudo-reference; in A3-B3-C3, we simplyuse the PTR method coupled with the reference set of all six arrays. Wesee that the invariant-set is more sensitive to the perturbed referencearray Exp03 R1* (A1) and it performs well if an appropriate reference isselected (A2). The quantile method shows a similar but less severephenomenon when the quantile-quantile transformation is based on thearray Exp03_R1* In contrast, the quantile normalization using averagequintiles as the pseudo-reference is more resistant to thisperturbation. For the sub-array normalization, the perturbation does notaffect the ratio estimates, since the normalization transformations aredone in each sub-window which greatly reduce the effects of this globalnoise.

The PTR method improves the results in all three normalizationalgorithms. We see that the log-ratios of spike-in genes are more closeto the expected log-ratio value M=1 and, and non-spike-in genes havesmaller variations along M=0. The PTR method deals with the singleperturbed reference array Exp03_R1 well, and it estimates the finaltranscript abundance robustly.

Variation Reduction by the PTR Method

We see that the PTR method achieves smaller variances for thenon-spike-in genes in the M-A plots of the perturbed data set. Tomeasure the effectiveness of the PTR method in variation reduction, wecompare it with other pre-processing methods using “Expt-3-4” data set.The non-spike-in genes are expected to have the same expression in bothexperiment 3 and 4, and the differences between them are due to thenon-biological factors. We preprocess six arrays with different methodsof normalization and summarization and estimate the expression valuesfor both experiment 3 and 4. In the M-A plots, we fit loess curves tothe absolute values of M against A using non-spike-in genes only. Theresult curves shown in FIG. 8 measure the variations of non-spike-ingenes between two experiments. The left, middle, and right column showthe results from the invariant-set, quantile, and sub-arraynormalization method respectively. Except for the PTR method, wesummarize the normalized results using the expresso function in the affypackage with either the Li-Wong's MBEI or the median polish method. Fromthe plots, we can see that the PTR method achieves the smallestvariations for each normalization algorithm.

In the left plot, we use the invariant-set normalization for both thePTR method and the other single-reference methods. The plot shows thatthe same pre-processing method but with different reference choicesresults in different variation curves. The PTR method reduces thebackground noise significantly.

In the middle plot, we use the quantile normalization, taking each rawarray as well as the average quantiles to be the reference. The plotshows substantial improvement by the PTR method, while the quantilesnormalization achieves a moderate performance using the averagequantiles as the pseudo-reference. The PTR method gives a betterstrategy to use the complete data information.

In the right plot of FIG. 8, we use the sub-array normalization, and theplot shows the improvement by the PTR method once again. Furthermore, weclearly see two different types of curves from the single-referenceresults. Each reference array from experiment 3 performs better at thelow intensity range but worse in the high intensity range; whereas eachfrom experiment 4 performs slightly better in the high intensity rangebut worse in the low intensity range. A similar yet less prominentpattern also exists in the results using the invariant-set and quantilenormalization. Replicates within either experiment 3 or 4 are similar,but arrays from two experiments lead to more different results. The PTRmethod takes into account reference arrays from both experiments,combines two types of expression results and gives the smallestvariation in both low and high intensity ranges.

The loess assessment has demonstrated that the PTR method can reducedthe variation significantly for the invariant-set, quantile andsub-array normalization method. This variation reduction, especially inthe low intensity range, is particularly valuable in the measurement ofgene expressions.

Improvement on Detection of Differentially Expressed Genes

In order to ensure that deferential gene detection is not sacrificed inthe effort to reduce the variation by the PTR method in expressionanalysis, we compute the receiver operating characteristic (ROC) curvesusing the HG-U133A data set. We conduct two comparative studies on thisdata set. In the first study, we compare every two experiments which arenext to each other in the Latin square design. Each pair of experimentshave 36 spike-in genes with 2-fold change. In the second study, wecompare every two experiments which are separated by one and exactly oneexperiment. Each pair of experiments have 36 spike-in genes with 4-foldchange. In total, we have 14 pairs of experiments in each study. Thecurves computed by the ROC package from Bioconductor are shown at thetop of FIG. 9. We compare the PTR method with various pre-processingcombinations in the expresso function of the affy package, whichincludes: invariant-set normalization plus Li-Wong's MBEI or medianpolish summarization; quantile normalization plus median polishsummarization with or without RMAs background correction. We see thatthe PTR method does equally well with both the quantile andinvariant-set normalization algorithm in this data set. The PTR methodgives the best performance in the detection of the differentiallyexpressed genes.

In addition, we make the similar comparisons on the “golden spike” dataset. We set the differentially expressed genes using fold changethreshold to 1.2 or 1.7. The ROC curves are shown at the bottom of theFIG. 9. We can see that the PTR method performs better with theinvariant-set normalization than the quantile normalization method.However, both of them outperform the other pre-processing methods.

The assessment on both data sets demonstrates that the PTR methodprovides higher specificity and sensitivity. The noise reductionimproves the detection of deferentially expressed genes.

Discussion

We explicitly address the reference issue in pre-processing expressionmicroarray and propose the PTR method to carry out the normalization andsummarization jointly. The PTR method can be applied to existingnormalization methods, including the invariant-set, sub-array, andquantile. It is the first time we propose a practical scheme toimplement the sub-array normalization. The sub-array takes into accountthe spatial pattern of hybridization, and can properly normalize themajority of probe intensities even in the presence of scratches orserious non-homogeneous hybridization. The PTR method enhances thisability using multiple references in the normalization and implicitlyselecting a “reference” at the probe-set level during summarization.

In this Example, we have discussed the experiment design withreplicates. Special attention needs to be paid when an experiment has noreplicates. We have not discussed the background correction issue, butthe existing background correction methods can be implemented before thenormalization step of the PTR method. Interestingly, we have shown thatthe PTR method reduces the variation of non-differentially expressedgenes, especially in the low intensity range. As a consequence, weimprove the signal-to-noise ratio, and we increase the detection powerof the deferentially expressed genes. The improvement is achievedwithout any additional information.

We include all arrays in the reference set and use the cross strategy toselect the corresponding target arrays in this paper. We are aware thatthey may not be the optimal strategy for reference and target selection.However, the PTR method can protect against and detect abnormal arrays.First, by using the robust LAD method in the summarization, we canaccurately estimate the transcript abundance as long as the majority ofnormalization results are right. Second, we can evaluate the arrayquality by the reference effect distribution, as shown in FIG. 11. Thearray showing distinct distribution from other arrays is likely a badcandidate for reference and may be excluded from the reference set inthe next-round PTR processing.

Although the present invention has been described in terms of specificexemplary embodiments and examples, it will be appreciated that theembodiments disclosed herein are for illustrative purposes only andvarious modifications and alterations might be made by those skilled inthe art without departing from the spirit and scope of the invention asset forth in the following claims.

1. A method of analyzing microarray data, comprising the steps of:providing a set of microarray data; grouping the microarray data intoreference data and target data; normalizing the microarray data byapplying a least trimmed squares regression method or a symmetricvariant thereof to determine parameters for a linear model that fits thedata; and analyzing the normalized microarray data to obtain a desiredresult.
 2. The method of claim 1, wherein the microarray is one selectedfrom the group consisting of oligonucleotide arrays, cDNA arrays, beadarrays, pathway arrays, ChIP-chip experiments, methylation arrays, exonarray, tissue arrays and protein arrays.
 3. The method according toclaim 2, wherein the microarray is an oligonucleotide array and whereinall data points from the oligonucleotide probes are used for the leasttrimmed squares normalization.
 4. The method according to claim 3,wherein the microarray data are from a set of duplicate microarrays, andwherein at least one of the duplicate microarrays is treated with areference sample and at least one of the duplicate microarrays istreated with a target sample.
 5. The method according to claim 2,wherein the microarray is an oligonucleotide array and wherein only datapoints from the perfectly matched probe oligonucleotides are used forthe least trimmed squares normalization.
 6. The method according toclaim 2, wherein the microarray is an oligonucleotide array and whereinonly data points from external controls or only data points from probeson the same array but not for the same organisms are used for the leasttrimmed square normalization.
 7. The method of claim 1, wherein theleast trimmed squares method uses a trimming fraction larger than thefraction of differentiated probes.
 8. The method of claim 1 furthercomprising a step of dividing each microarray into subarrays, andwherein said normalization is performed within each subarray.
 9. Themethod of claim 8, wherein each subarray has a size of from about 10×10data points to a size smaller than the whole array.
 10. The method ofclaim 9, wherein the subarrays are allowed to overlap each other. 11.The method of claim 10, wherein the subarrays overlap each other fromabout 0% to any percentage less than 100%.
 12. A method for analyzingmicroarray data, comprising the steps of: providing a set of microarraydata; subdividing the microarray data into subarrays; normalizing themicroarray data within each subarray; and analyzing the normalized datato obtain a desired result.
 13. The method according to claim 12,wherein the microarray data is from a plurality of duplicatemicroarrays.
 14. The method according to claim 12, wherein each subarrayhas a size from about 10×10 data points to a size smaller than the wholearray.
 15. The method according to claim 12, wherein adjacent subarraysare allowed to overlap each other.
 16. The method according to claim 12,wherein the step of analyzing comprises applying a method selected fromestimation, testing, validating, clustering, or discrimination.
 17. Amethod for obtaining expression profiles from microarray experimentswhich streamlines normalization and summarization of data, comprisingthe steps of: providing a set of microarray data from duplicatemicroarrays wherein at least one microarray is treated with treatmentsample and at least one microarray is treated with control sample;selecting a plurality of reference arrays from among the microarrays anda plurality of corresponding target arrays from among the remainingmicroarrays according to a design of the microarray experiment; applyinga normalization procedure to each pair of reference and targetmicro-arrays; summarizing the expression value for each probe-set fromnormalized microarray and reference array data according to aprobe-treatment-reference (PTR) model, and estimating the parameters inthe PTR model by a Least Absolute Deviations approach, whereby the stepsof normalization and summarization are streamlined.
 18. The method ofclaim 17, wherein multiple treatment levels are allowed for microarraytreatment.
 19. The method of claim 17, wherein said normalization is bya least trimmed squares regression method.
 20. The method of claim 17,wherein all microarrays are included in the reference set; and, for eachreference, all the other microarrays are its targets.
 21. The method ofclaim 17, wherein the plurality of reference and target arrays areselected such that all microarrays treated with control sample areincluded in the reference set, and for each reference that is treatedwith control sample, replicates from arrays treated with treatmentsample are taken as its target arrays.
 22. A method for detectingdefective areas on a microarray, comprising: dividing the array into aplurality of subarrays; applying a normalization procedure comprising aleast trimmed squares method or a symmetric variant thereof, whereinsaid least trimmed squares regression method or the symmetric variantthereof normalizes the microarray data by estimating parameters for alinear model and fitting the data to the model; and estimating theparameters of the linear models across the plurality of subarrays todetect subarrays that are defective.
 23. A method for salvaging datafrom a defective micro-array, comprising: applying the method of claim22 to identify areas of the microarray that are defective; and savingdata from non-defective areas of the microarray for later processing,thereby, salvaging data from a defective micro-array.
 24. A computerimplemented system for normalizing microarray data, comprising: a datainput for receiving microarray data and user input; a processing unitand a memory configured to normalize the microarray data by performing aleast trimmed squares method or a symmetric variant thereof on the data,wherein the least trimmed squares method or variant thereof determinesparameters for a linear model that fit the data and normalizes the databased on the model; and outputting the resulting normalized microarraydata for further analysis.
 25. The system of claim 24, wherein theprocessing unit and memory are configured to further perform the step ofsubdividing the microarray data into subarrays before performing thenormalizing step within each subarray.
 26. A computer implemented systemfor summarizing gene expression from normalized microarrays, comprising:a graphical interface capable of taking as input raw and normalizedmicroarray data and allowing users to set reference index and treatmentindex on the data; a processing unit and a memory configured tosummarize the data according to the PTR model by performing medianpolishing; and outputting the resulting expression profiles in standardfiles for further analysis.
 27. A computer readable medium havingencoded thereon a method according to claim 1, 12, 17, 22, or 23.